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- EMDB-7476: Cdc48-Npl4 complex in the presence of ATP-gamma-S -

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Basic information

Entry
Database: EMDB / ID: EMD-7476
TitleCdc48-Npl4 complex in the presence of ATP-gamma-S
Map dataprimary map
Sample
  • Organelle or cellular component: Cdc48-Npl4/Ufd1 complex
    • Protein or peptide: Npl4
    • Protein or peptide: Putative cell division control protein
  • Ligand: ZINC ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsAAA+ / ERAD / zinc finger / ubiquitin-binding protein / MOTOR PROTEIN
Function / homology
Function and homology information


nuclear protein quality control by the ubiquitin-proteasome system / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / retrograde protein transport, ER to cytosol / polyubiquitin modification-dependent protein binding / autophagosome maturation / mRNA transport / ubiquitin binding / protein transport / ubiquitin-dependent protein catabolic process ...nuclear protein quality control by the ubiquitin-proteasome system / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / retrograde protein transport, ER to cytosol / polyubiquitin modification-dependent protein binding / autophagosome maturation / mRNA transport / ubiquitin binding / protein transport / ubiquitin-dependent protein catabolic process / nuclear membrane / mitochondrial outer membrane / cell division / ubiquitin protein ligase binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : ...NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / Vps4 oligomerisation, C-terminal / Vps4 C terminal oligomerisation domain / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / MPN domain / MPN domain profile. / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nuclear protein localization protein 4 / Putative cell division control protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKim KH / Bodnar NO
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.
Authors: Nicholas O Bodnar / Kelly H Kim / Zhejian Ji / Thomas E Wales / Vladimir Svetlov / Evgeny Nudler / John R Engen / Thomas Walz / Tom A Rapoport /
Abstract: Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains ...Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains two stacked ATPase rings (D1 and D2) and six N-terminal (N) domains. Cdc48 binds various cofactors, including the Ufd1-Npl4 heterodimer. Here, we report structures of the Cdc48-Ufd1-Npl4 complex from Chaetomium thermophilum. Npl4 interacts through its UBX-like domain with a Cdc48 N domain, and it uses two Zn-finger domains to anchor the enzymatically inactive Mpr1-Pad1 N-terminal (MPN) domain, homologous to domains found in several isopeptidases, to the top of the D1 ATPase ring. The MPN domain of Npl4 is located above Cdc48's central pore, a position similar to the MPN domain from deubiquitinase Rpn11 in the proteasome. Our results indicate that Npl4 is unique among Cdc48 cofactors and suggest a mechanism for binding and translocation of polyubiquitinated substrates into the ATPase.
History
DepositionFeb 22, 2018-
Header (metadata) releaseMar 7, 2018-
Map releaseJul 4, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6chs
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7476.png

Downloads & links

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Map

FileDownload / File: emd_7476.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 256 pix.
= 332.8 Å		1.3 Å/pix.
x 256 pix.
= 332.8 Å		1.3 Å/pix.
x 256 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.065897405 - 0.16063109
Average (Standard dev.)0.0005993301 (±0.005306914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0660.1610.001

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Supplemental data

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Sample components

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Entire : Cdc48-Npl4/Ufd1 complex

EntireName: Cdc48-Npl4/Ufd1 complex
Components
  • Organelle or cellular component: Cdc48-Npl4/Ufd1 complex
    • Protein or peptide: Npl4
    • Protein or peptide: Putative cell division control protein
  • Ligand: ZINC ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cdc48-Npl4/Ufd1 complex

SupramoleculeName: Cdc48-Npl4/Ufd1 complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Chaetomium thermophilum (fungus)

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Macromolecule #1: Npl4

MacromoleculeName: Npl4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 73.880391 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLLRMRCPDG MFRLTVEKDD TFGELVRQLV PKLPPTVDPK SITLSNHPSG GDSKRIDEIA RFKIGQVGHG DLIFVRYQTS DTVANGRSV DISSQTAGLS SSANRLNGKP VLPTEDHPID PPPNTSAERI KNPWEVVRQS PLDDRLDKLD GKIPRKRGAM C RHGPKGMC ...String:
MLLRMRCPDG MFRLTVEKDD TFGELVRQLV PKLPPTVDPK SITLSNHPSG GDSKRIDEIA RFKIGQVGHG DLIFVRYQTS DTVANGRSV DISSQTAGLS SSANRLNGKP VLPTEDHPID PPPNTSAERI KNPWEVVRQS PLDDRLDKLD GKIPRKRGAM C RHGPKGMC DYCTPLDPFN PQYLEEKKIK YMSVHAYMRK INSATNRPEL GSSFIPPLVE PYYRVKRDCP SGHPQWPEGI CT KCQPSAI TLQPQPFRMV DHVEFASPQI IDRFLDAWRR TGVQRLGILY GRYLEYDAVP LGIKAVVEAI YEPPQVDEID GIT LNPWEN EQEVNQVAKY CGLEQVGVIW TDLLDAGKGD GSVVCKRHAD SYFLAAQEIV FAARLQAQHP KPSKWSDTGR FGSN FVTCV VSGNEQGEIS ISAYQMSNDA VEMVRADIIE PSADPTLMLV REEEEDDGSP SKTRYIPEVF YRKINEYGAN VLENA KPAF PVEYLFVTLT HGFPDSPSPL FTDNIFPIEN REYVGEAQEV SAVAKALKVH EADAPMNVSD FHLLCFIHQM SVLSKE EEA LLCRVATLHD LAESFQLRST TGWQTLHMIL QSTGERVPKR PRFSDNVPSS SQDTQEALGG NNLDPGEPLA KRFAAVR LN ENNQSSPKPY APSRWNL

UniProtKB: Nuclear protein localization protein 4

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Macromolecule #2: Putative cell division control protein

MacromoleculeName: Putative cell division control protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 90.432516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAPESKDHKK KVNLTDPSGA EHREENDTAT AILKKKKKPN QLMVTDAVND DNSIIALSNN TMEALQLFRG DTVLVRGKKR RDTVLIVLA DDDLDDGSAR INRVVRHNLR VKHGDMITIH PCPDIKYAKR IAVLPIADTV EGLTGSLFDV FLAPYFREAY R PVRQGDLF ...String:
MAPESKDHKK KVNLTDPSGA EHREENDTAT AILKKKKKPN QLMVTDAVND DNSIIALSNN TMEALQLFRG DTVLVRGKKR RDTVLIVLA DDDLDDGSAR INRVVRHNLR VKHGDMITIH PCPDIKYAKR IAVLPIADTV EGLTGSLFDV FLAPYFREAY R PVRQGDLF TVRGGMRQVE FKVVEVDPPE YGIVAQDTII HCEGEPIPRE EEENNLNEVG YDDIGGCRKQ LAQIREMVEL PL RHPQLFK SIGIKPPRGV LLYGPPGTGK TLMARAVANE TGAFFFLING PEIMSKMAGE SESNLRKAFE EAEKNSPAII FID EIDSIA PKREKTNGEV ERRVVSQLLT LMDGMKARSN VVVMAATNRP NSIDPALRRF GRFDREVDIG IPDPTGRLEI LQIH TKNMK LADDVDLEQI AAETHGYVGS DLAALCSEAA MQQIREKMDL IDLDEDTIDA EVLDSLGVTM DNFRYALGVS NPSAL REVA VVEVPNVRWE DIGGLEQVKQ ELKEQVQYPV DHPEKFLKFG LSPSRGVLFY GPPGTGKTML AKAVANECAA NFISVK GPE LLSMWFGESE SNIRDIFDKA RAAAPCVVFL DELDSIAKAR GGSIGDAGGA SDRVVNQLLT EMDGMTSKKN VFVIGAT NR PEQLDPALCR PGRLDQLIYV PLPDEAGRLS ILKAQLRKTP VSKDVDLAYI ASKTHGFSGA DLAFITQRAV KLAIKESI A AEIERQKARE AAGEDVNMED DEDPVPELTK RHFEEAMRDA RRSVSDVEIR RYEAFAQQMK NAGPGAFFKF PDSTTDNSA SNAAGNSFGD AGNDDDLYT

UniProtKB: Putative cell division control protein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 12 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMHEPES
150.0 mMsodium chlorideNaCl
5.0 mMmagnesium chlorideMgCl2
0.5 mMTCEP
100.0 uMATPgS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 9299 / Average exposure time: 15.0 sec. / Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 808059
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 91883
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6chs:
Cdc48-Npl4 complex in the presence of ATP-gamma-S

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